Thanks a lot Justin and Mark for your useful input.
Indeed Justin was right, the quest to dissect the total energy of the system to get that contributed by the protein alone was not trivial at all! I missed out this thread yesterday http://www.mail-archive.com/gmx-users@gromacs.org/msg34610.html as well as Mark's trick to decompose bonded terms by hacking the .top file. (However, I read from http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy that the Coul-recip term is not decomposable regardless of the tricks used...) Mark, following your advice, I added -nsteps 0 (-1 didn't work) to tpbconv. I managed to get the interactive prompt succesfully this time. Reading toplogy and shit from rerun1.tpr Reading file rerun1.tpr, VERSION 4.0.7 (single precision) Setting nsteps to 0 Group 0 ( System) has 100581 elements Group 1 ( Protein) has 4002 elements Group 2 ( Protein-H) has 3145 elements Group 3 ( C-alpha) has 412 elements Group 4 ( Backbone) has 1236 elements Group 5 ( MainChain) has 1649 elements Group 6 (MainChain+Cb) has 2027 elements Group 7 ( MainChain+H) has 2039 elements Group 8 ( SideChain) has 1963 elements Group 9 ( SideChain-H) has 1496 elements Group 10 ( Prot-Masses) has 4002 elements Group 11 ( Non-Protein) has 96579 elements Group 12 ( POPE) has 13052 elements Group 13 ( SOL) has 83523 elements Group 14 ( CL-) has 4 elements Group 15 ( Other) has 96579 elements Group 16 ( SOL_CL-) has 83527 elements Group 17 (Protein_POPE) has 17054 elements Select a group: As suggested, I have also tried to compare the (average) values of subset.tpr and fullsystem.tpr, these are the total energies of: 1) System= -1.28209 e+06 2) Protein= -9571.86 3) Lipid= -296121 4) SOL_CL= -821353 5) Other= -1.22684e+06 It was found that the: 1) Total energies (Protein + lipid + SOL_CL-) not equal to total energy of the system 2) Total energies of (Lipid + SOL_CL-) not equal to total energy of other 3) Total energies of (others + protein) not equal to total energy of the system I have yet to work out the reasons for the discrepancies, will spend some time pondering and trying to make sense of these (and other) values. Thanks a bunch again! HW From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Wednesday, November 10, 2010 9:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun -rerun: bonded interactions of protein On 10/11/2010 11:29 PM, NG HUI WEN wrote: Hi Gmxusers, I have been trying to run mdrun -rerun to get the energy of the protein in my protein-lipid system. I know similar questions have been raised on this topic before, I have tried to glean useful information from them to solve my problem but unfortunately to no avail. Thanks for your patience! As I did not have energygrps in the initial .mdp file, I included it this time integrator = md nsteps = 0 dt = 0.002 nstxout = 50000 nstvout = 50000 nstenergy = 500 nstlog = 500 Continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein POPE SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 pbc = xyz DispCorr = EnerPres gen_vel = no nstcomm = 1 comm-mode = Linear comm-grps = Protein_POPE SOL_CL- energygrps = Protein SOL POPE I then did 1)grompp -f new.mdp -n index.ndx -c old.tpr -o rerun.tpr -p topol.top 2)trjconv -f old.trr -n index.ndx -s rerun.tpr -o rerun.trr (when prompted, I selected "0" system) 3)mdrun -s rerun.tpr -rerun rerun.trr I notice that the previous post http://oldwww.gromacs.org/pipermail/gmx-users/2009-January/038968.html suggested to use tpbconv (on rerun.tpr) and trjconv (on rerun.trr) to extract the protein only. While it was possible to do so with trjconv, it wasn't feasible with tpbconv (I'm using gromacs 4.0.7) - I might have missed out something as I did not get any prompt/output (see below) tpbconv -s topol.tpr -n index_P.ndx -o rerun2.tpr Reading toplogy and shit from topol.tpr Reading file topol.tpr, VERSION 4.0.7 (single precision) 0 steps (0 ps) remaining from first run. You've simulated long enough. Not writing tpr file Looking at the code, tpbconv checks for whether there are any more steps to simulate before even considering letting you use it in the "create subset" mode. You could argue that this is buggy, because the way it computes whether there are any more steps will always indicate no more steps in such cases. However, the workaround is to use tpbconv -nsteps -1 (as well as the other stuff). Let me know how this goes and I'll update the documentation. Using the g_energy command on the output energy.edr file, I got among others, these options to choose 49 Coul-SR:Protein-Protein 50 LJ-SR:Protein-Protein 51 Coul-14:Protein-Protein 52 LJ-14:Protein-Protein In order to get the energy of the protein, I reckon I have to add 49,50,51,52 (to account for the nonbonded components) and I think that you can make a case either way for 1-4 interactions - they're algorithmically similar to the other non-bonded interactions, but their parameter values should be tightly coupled to some other of the bonded parameters, but then in several forcefields those values are just scaled versions of the normal ones... I'd guess most people call them non-bonded. 1 Angle 2 G96Angle 3 Proper-Dih. 4 Ryckaert-Bell. 5 Improper-Dih for the bonded components. However, I think 1-5 is the bonded terms for the system and not the protein alone. Can anyone help me with this? Compare values from reruns on the subset-tpr and the full-tpr. I don't know whether/how well that works. In extremis, you should be able to reduce the .tpr to a single interaction. Also, on a slightly different note, this post http://oldwww.gromacs.org/pipermail/gmx-users/2005-July/016307.html suggested that the force constant of the solvent (DMSO) to be adjusted to zero. Am I right to think that it does not apply to my case as my protein-lipid system is solvated with SPC? (I read that SPC is rigid water. I did not add -DFLEXIBLE in .mdp) That was in the context of a full-tpr rerun. The point is that atoms that have been constrained don't contribute to relevant sums. Because you are using constraints, there's no "Bonds" energy sum for any atom pair. Because the DMSO was a flexible model, its bonded-interactions contributions need to be subtracted (i.e. parameters set to zero) to get a group-wise bonded-interaction value. Mark Any help would be highly appreciated.Thanks! 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